data_15047 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Ubiquitin in 8 M Urea ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Meier Sebastian . . 2 Strohmeier Mark . . 3 Blackledge Martin . . 4 Grzesiek Stephan . . stop_ _BMRB_accession_number 15047 _BMRB_flat_file_name bmr15047.str _Entry_type new _Submission_date 2006-11-21 _Accession_date 2006-11-21 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details "Ubiquitin in 8 M Urea, pH 2.5, 298 K" loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 71 "1H chemical shifts" 72 "15N chemical shifts" 72 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2007-05-09 update BMRB "complete entry citation" 2006-12-11 original author "original release" stop_ loop_ _Related_BMRB_accession_number _Relationship 4375 "more complete shift set at slightly different conditions" stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title ; Direct Observation of Dipolar Couplings and Hydrogen Bonds across a beta-hairpin in 8 M Urea ; _Citation_status published _Citation_type journal _PubMed_ID 17243799 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Meier Sebastian . . 2 Strohmeier Mark . . 3 Blackledge Martin . . 4 Grzesiek Stephan . . stop_ _Journal_abbreviation "J. Am. Chem. Soc." _Journal_volume 129 _Journal_issue 4 _Page_first 754 _Page_last 755 _Year 2007 save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "denatured ubiquitin" _Abbreviation_common "denatured ubiquitin" loop_ _Mol_system_component_name _Mol_label ubiquitin $denatured_ubiquitin stop_ _System_physical_state denatured _System_oligomer_state monomer _System_paramagnetic no save_ ######################## # Monomeric polymers # ######################## save_denatured_ubiquitin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common denatured_ubiquitin _Mol_thiol_state "not present" ############################## # Polymer residue sequence # ############################## _Residue_count 76 _Mol_residue_sequence ; MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG ; loop_ _Residue_seq_code _Residue_label 1 MET 2 GLN 3 ILE 4 PHE 5 VAL 6 LYS 7 THR 8 LEU 9 THR 10 GLY 11 LYS 12 THR 13 ILE 14 THR 15 LEU 16 GLU 17 VAL 18 GLU 19 PRO 20 SER 21 ASP 22 THR 23 ILE 24 GLU 25 ASN 26 VAL 27 LYS 28 ALA 29 LYS 30 ILE 31 GLN 32 ASP 33 LYS 34 GLU 35 GLY 36 ILE 37 PRO 38 PRO 39 ASP 40 GLN 41 GLN 42 ARG 43 LEU 44 ILE 45 PHE 46 ALA 47 GLY 48 LYS 49 GLN 50 LEU 51 GLU 52 ASP 53 GLY 54 ARG 55 THR 56 LEU 57 SER 58 ASP 59 TYR 60 ASN 61 ILE 62 GLN 63 LYS 64 GLU 65 SER 66 THR 67 LEU 68 HIS 69 LEU 70 VAL 71 LEU 72 ARG 73 LEU 74 ARG 75 GLY 76 GLY stop_ _Sequence_homology_query_date 2009-06-13 _Sequence_homology_query_revised_last_date 2009-06-06 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 1YX5 "Solution Structure Of S5a Uim-1UBIQUITIN COMPLEX" 100.00 98 100.00 100.00 1.84e-36 PDB 1YX6 "Solution Structure Of S5a Uim-2UBIQUITIN COMPLEX" 100.00 98 100.00 100.00 1.84e-36 DBJ BAA09860 "polyubiquitin [Homo sapiens]" 100.00 611 98.68 98.68 4.70e-35 DBJ BAA11842 "ubiquitin [Cavia porcellus]" 100.00 311 100.00 100.00 6.24e-36 DBJ BAA11843 "ubiquitin extention protein [Cavia porcellus]" 100.00 156 100.00 100.00 1.25e-36 DBJ BAA76675 "ubiquitin/79aa fusion protein [Bombyx mori]" 100.00 155 98.68 100.00 4.90e-36 DBJ BAA83996 "ubiquitin [Canis lupus familiaris]" 100.00 128 100.00 100.00 1.57e-36 EMBL CAA30815 "unnamed protein product [Cricetulus sp.]" 93.42 223 100.00 100.00 9.88e-33 EMBL CAA37227 "unnamed protein product [Drosophila melanogaster]" 100.00 128 100.00 100.00 1.75e-36 EMBL CAA37599 "unnamed protein product [Manduca sexta]" 100.00 155 100.00 100.00 1.67e-36 EMBL CAA40312 "ubiquitin-52 amino acid fusion protein [Homo sapiens]" 100.00 128 100.00 100.00 1.57e-36 EMBL CAA40313 "ubiquitin-52 amino acid fusion protein [Homo sapiens]" 100.00 128 100.00 100.00 1.57e-36 GenBank AAA28997 ubiquitin 100.00 231 100.00 100.00 6.08e-36 GenBank AAA28998 "ubiquitin-hybrid protein precursor" 100.00 156 100.00 100.00 2.00e-36 GenBank AAA53067 "p125 protein" 100.00 1054 100.00 100.00 1.88e-36 GenBank AAA56988 "ubiquitin [synthetic construct]" 100.00 128 100.00 100.00 1.57e-36 GenBank AAA57047 "ubiquitin [synthetic construct]" 100.00 157 100.00 100.00 1.23e-36 PIR I65237 "ubiquitin / ribosomal protein L40, cytosolic [validated] - rat" 100.00 128 100.00 100.00 1.57e-36 PIR UQHUR7 "ubiquitin / ribosomal protein S27a, cytosolic [validated] - human" 100.00 156 100.00 100.00 1.25e-36 REF NP_001005123 "ubiquitin A-52 residue ribosomal protein fusion product 1 [Xenopus (Silurana) tropicalis]" 100.00 128 100.00 100.00 1.57e-36 REF NP_001009202 "polyubiquitin [Ovis aries]" 100.00 305 98.68 100.00 1.01e-35 REF NP_001009286 "ubiqitin RPL40 fusion protein [Ovis aries]" 100.00 128 100.00 100.00 1.57e-36 REF NP_001016172 "hypothetical protein LOC548926 [Xenopus (Silurana) tropicalis]" 100.00 156 100.00 100.00 1.25e-36 REF NP_001029037 "ribosomal protein S27a [Mus musculus]" 100.00 156 100.00 100.00 1.68e-36 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $denatured_ubiquitin Human 9606 Eukaryota Metazoa Homo sapiens stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $denatured_ubiquitin "recombinant technology" ? ? ? BL21DE3 pET21b+ stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $denatured_ubiquitin 2.5 mM "[U-13C; U-15N; U-2H]" H2O 55.5 M "natural abundance" D2O 5 % [U-2H] urea 8 M "natural abundance" stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe loop_ _Vendor _Address _Electronic_address "Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax" ? ? stop_ loop_ _Task processing stop_ save_ save_PIPP _Saveframe_category software _Name PIPP loop_ _Vendor _Address _Electronic_address Garrett ? ? stop_ loop_ _Task "data analysis" stop_ save_ save_xwinnmr _Saveframe_category software _Name xwinnmr loop_ _Vendor _Address _Electronic_address "Bruker Biospin" ? ? stop_ loop_ _Task collection stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_nmr_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 save_ save_nmr_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 800 _Details "TCI cryoprobe" save_ ############################# # NMR applied experiments # ############################# save_3D_HN(CO)CA_1 _Saveframe_category NMR_applied_experiment _Experiment_name "3D HN(CO)CA" _Sample_label $sample_1 save_ save_3D_HNCA_2 _Saveframe_category NMR_applied_experiment _Experiment_name "3D HNCA" _Sample_label $sample_1 save_ save_3D_HNCO_3 _Saveframe_category NMR_applied_experiment _Experiment_name "3D HNCO" _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name "2D 1H-15N HSQC" _Sample_label $sample_1 save_ save_3D_1H-15N_ROESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name "3D 1H-15N ROESY" _Sample_label $sample_1 save_ save_3D_15N_HNHN-COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name "3D 15N HNHN-COSY" _Sample_label $sample_1 save_ save_3D_HNCACB_7 _Saveframe_category NMR_applied_experiment _Experiment_name "3D HNCACB" _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 ? K pH 2.5 ? pH pressure 1 ? atm "ionic strength" 20 ? mM stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 "methyl protons" ppm 0.00 internal direct ? ? ? 1.000000000 DSS C 13 "methyl protons" ppm 0.00 n/a indirect ? ? ? 0.251449530 DSS N 15 "methyl protons" ppm 0.00 n/a indirect ? ? ? 0.101329118 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # Index Value Definition # # # # 1 Unique (geminal atoms and geminal methyl # # groups with identical chemical shifts # # are assumed to be assigned to # # stereospecific atoms) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. Tyr HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. Lys HG and # # HD protons or Trp HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (Lys 12 vs. Lys 27) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name ubiquitin loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 MET CA C 55.02 0.1 1 2 2 2 GLN H H 8.81 0.1 1 3 2 2 GLN CA C 55.63 0.1 1 4 2 2 GLN N N 123.77 0.1 1 5 3 3 ILE H H 8.25 0.1 1 6 3 3 ILE CA C 60.50 0.1 1 7 3 3 ILE N N 122.35 0.1 1 8 4 4 PHE H H 8.39 0.1 1 9 4 4 PHE CA C 57.14 0.1 1 10 4 4 PHE N N 124.41 0.1 1 11 5 5 VAL H H 8.24 0.1 1 12 5 5 VAL CA C 61.71 0.1 1 13 5 5 VAL N N 122.28 0.1 1 14 6 6 LYS H H 8.35 0.1 1 15 6 6 LYS CA C 56.13 0.1 1 16 6 6 LYS N N 124.98 0.1 1 17 7 7 THR H H 8.24 0.1 1 18 7 7 THR CA C 61.51 0.1 1 19 7 7 THR N N 115.83 0.1 1 20 8 8 LEU H H 8.4 0.1 1 21 8 8 LEU CA C 55.38 0.1 1 22 8 8 LEU N N 124.07 0.1 1 23 9 9 THR H H 7.99 0.1 1 24 9 9 THR CA C 61.58 0.1 1 25 9 9 THR N N 112.63 0.1 1 26 10 10 GLY H H 8.21 0.1 1 27 10 10 GLY CA C 45.17 0.1 1 28 10 10 GLY N N 110.11 0.1 1 29 11 11 LYS H H 8.02 0.1 1 30 11 11 LYS CA C 56.11 0.1 1 31 11 11 LYS N N 120.23 0.1 1 32 12 12 THR H H 8.27 0.1 1 33 12 12 THR CA C 62.01 0.1 1 34 12 12 THR N N 116.44 0.1 1 35 13 13 ILE H H 8.32 0.1 1 36 13 13 ILE CA C 60.73 0.1 1 37 13 13 ILE N N 123.3 0.1 1 38 14 14 THR H H 8.21 0.1 1 39 14 14 THR CA C 61.55 0.1 1 40 14 14 THR N N 118.58 0.1 1 41 15 15 LEU H H 8.28 0.1 1 42 15 15 LEU CA C 54.71 0.1 1 43 15 15 LEU N N 124.96 0.1 1 44 16 16 GLU H H 8.36 0.1 1 45 16 16 GLU CA C 55.36 0.1 1 46 16 16 GLU N N 121.4 0.1 1 47 17 17 VAL H H 8.15 0.1 1 48 17 17 VAL CA C 61.92 0.1 1 49 17 17 VAL N N 121.36 0.1 1 50 18 18 GLU H H 8.34 0.1 1 51 18 18 GLU N N 124.26 0.1 1 52 19 19 PRO CA C 63.12 0.1 1 53 20 20 SER H H 8.33 0.1 1 54 20 20 SER CA C 58.35 0.1 1 55 20 20 SER N N 115.18 0.1 1 56 21 21 ASP H H 8.42 0.1 1 57 21 21 ASP CA C 52.86 0.1 1 58 21 21 ASP N N 120.31 0.1 1 59 22 22 THR H H 8 0.1 1 60 22 22 THR CA C 62.00 0.1 1 61 22 22 THR N N 113.9 0.1 1 62 23 23 ILE H H 8.04 0.1 1 63 23 23 ILE CA C 61.36 0.1 1 64 23 23 ILE N N 122.6 0.1 1 65 24 24 GLU H H 8.28 0.1 1 66 24 24 GLU CA C 55.50 0.1 1 67 24 24 GLU N N 123.53 0.1 1 68 25 25 ASN H H 8.4 0.1 1 69 25 25 ASN CA C 53.10 0.1 1 70 25 25 ASN N N 120.21 0.1 1 71 26 26 VAL H H 8.01 0.1 1 72 26 26 VAL CA C 62.31 0.1 1 73 26 26 VAL N N 120.02 0.1 1 74 27 27 LYS H H 8.26 0.1 1 75 27 27 LYS CA C 56.17 0.1 1 76 27 27 LYS N N 124.29 0.1 1 77 28 28 ALA H H 8.14 0.1 1 78 28 28 ALA CA C 52.28 0.1 1 79 28 28 ALA N N 124.84 0.1 1 80 29 29 LYS H H 8.23 0.1 1 81 29 29 LYS CA C 56.31 0.1 1 82 29 29 LYS N N 120.91 0.1 1 83 30 30 ILE H H 8.17 0.1 1 84 30 30 ILE CA C 60.98 0.1 1 85 30 30 ILE N N 122.38 0.1 1 86 31 31 GLN H H 8.44 0.1 1 87 31 31 GLN CA C 55.58 0.1 1 88 31 31 GLN N N 124.39 0.1 1 89 32 32 ASP H H 8.46 0.1 1 90 32 32 ASP CA C 52.86 0.1 1 91 32 32 ASP N N 120.67 0.1 1 92 33 33 LYS H H 8.35 0.1 1 93 33 33 LYS CA C 56.52 0.1 1 94 33 33 LYS N N 121.84 0.1 1 95 34 34 GLU H H 8.24 0.1 1 96 34 34 GLU CA C 55.73 0.1 1 97 34 34 GLU N N 120.23 0.1 1 98 35 35 GLY H H 8.25 0.1 1 99 35 35 GLY CA C 44.97 0.1 1 100 35 35 GLY N N 109.33 0.1 1 101 36 36 ILE H H 7.95 0.1 1 102 36 36 ILE N N 120.64 0.1 1 103 38 38 PRO CA C 63.33 0.1 1 104 39 39 ASP H H 8.38 0.1 1 105 39 39 ASP CA C 53.08 0.1 1 106 39 39 ASP N N 117.06 0.1 1 107 40 40 GLN H H 8.23 0.1 1 108 40 40 GLN CA C 55.90 0.1 1 109 40 40 GLN N N 120.02 0.1 1 110 41 41 GLN H H 8.17 0.1 1 111 41 41 GLN CA C 55.91 0.1 1 112 41 41 GLN N N 120.81 0.1 1 113 42 42 ARG H H 8.31 0.1 1 114 42 42 ARG CA C 56.00 0.1 1 115 42 42 ARG N N 122 0.1 1 116 43 43 LEU H H 8.24 0.1 1 117 43 43 LEU CA C 54.88 0.1 1 118 43 43 LEU N N 123.71 0.1 1 119 44 44 ILE H H 8.11 0.1 1 120 44 44 ILE CA C 60.69 0.1 1 121 44 44 ILE N N 121.74 0.1 1 122 45 45 PHE H H 8.33 0.1 1 123 45 45 PHE CA C 57.28 0.1 1 124 45 45 PHE N N 124.45 0.1 1 125 46 46 ALA H H 8.25 0.1 1 126 46 46 ALA CA C 52.22 0.1 1 127 46 46 ALA N N 125.79 0.1 1 128 47 47 GLY H H 7.8 0.1 1 129 47 47 GLY CA C 45.11 0.1 1 130 47 47 GLY N N 107.09 0.1 1 131 48 48 LYS H H 8.13 0.1 1 132 48 48 LYS CA C 56.29 0.1 1 133 48 48 LYS N N 120.24 0.1 1 134 49 49 GLN H H 8.42 0.1 1 135 49 49 GLN N N 121.28 0.1 1 136 50 50 LEU H H 8.27 0.1 1 137 50 50 LEU CA C 55.11 0.1 1 138 50 50 LEU N N 123.43 0.1 1 139 51 51 GLU H H 8.37 0.1 1 140 51 51 GLU CA C 55.55 0.1 1 141 51 51 GLU N N 120.44 0.1 1 142 52 52 ASP H H 8.43 0.1 1 143 52 52 ASP CA C 52.93 0.1 1 144 52 52 ASP N N 119.48 0.1 1 145 53 53 GLY H H 8.26 0.1 1 146 53 53 GLY CA C 45.41 0.1 1 147 53 53 GLY N N 108.42 0.1 1 148 54 54 ARG H H 8.04 0.1 1 149 54 54 ARG CA C 56.04 0.1 1 150 54 54 ARG N N 119.7 0.1 1 151 55 55 THR H H 8.17 0.1 1 152 55 55 THR CA C 61.77 0.1 1 153 55 55 THR N N 115.23 0.1 1 154 56 56 LEU H H 8.27 0.1 1 155 56 56 LEU CA C 55.07 0.1 1 156 56 56 LEU N N 124.29 0.1 1 157 57 57 SER H H 8.26 0.1 1 158 57 57 SER CA C 58.18 0.1 1 159 57 57 SER N N 115.85 0.1 1 160 58 58 ASP H H 8.35 0.1 1 161 58 58 ASP CA C 52.81 0.1 1 162 58 58 ASP N N 120.29 0.1 1 163 59 59 TYR H H 7.99 0.1 1 164 59 59 TYR CA C 58.00 0.1 1 165 59 59 TYR N N 119.82 0.1 1 166 60 60 ASN H H 8.26 0.1 1 167 60 60 ASN CA C 53.07 0.1 1 168 60 60 ASN N N 119.91 0.1 1 169 61 61 ILE H H 7.9 0.1 1 170 61 61 ILE CA C 61.13 0.1 1 171 61 61 ILE N N 120.48 0.1 1 172 62 62 GLN H H 8.29 0.1 1 173 62 62 GLN CA C 56.07 0.1 1 174 62 62 GLN N N 123.52 0.1 1 175 63 63 LYS H H 8.25 0.1 1 176 63 63 LYS CA C 56.46 0.1 1 177 63 63 LYS N N 122.39 0.1 1 178 64 64 GLU H H 8.31 0.1 1 179 64 64 GLU CA C 55.70 0.1 1 180 64 64 GLU N N 120.86 0.1 1 181 65 65 SER H H 8.34 0.1 1 182 65 65 SER CA C 58.31 0.1 1 183 65 65 SER N N 116.58 0.1 1 184 66 66 THR H H 8.16 0.1 1 185 66 66 THR CA C 61.78 0.1 1 186 66 66 THR N N 115.39 0.1 1 187 67 67 LEU H H 8.03 0.1 1 188 67 67 LEU CA C 55.21 0.1 1 189 67 67 LEU N N 123.59 0.1 1 190 68 68 HIS H H 8.57 0.1 1 191 68 68 HIS CA C 54.75 0.1 1 192 68 68 HIS N N 119.82 0.1 1 193 69 69 LEU H H 8.22 0.1 1 194 69 69 LEU CA C 54.95 0.1 1 195 69 69 LEU N N 123.93 0.1 1 196 70 70 VAL H H 8.31 0.1 1 197 70 70 VAL CA C 62.15 0.1 1 198 70 70 VAL N N 122.47 0.1 1 199 71 71 LEU H H 8.29 0.1 1 200 71 71 LEU CA C 54.73 0.1 1 201 71 71 LEU N N 126.62 0.1 1 202 72 72 ARG H H 8.41 0.1 1 203 72 72 ARG CA C 55.74 0.1 1 204 72 72 ARG N N 122.57 0.1 1 205 73 73 LEU H H 8.28 0.1 1 206 73 73 LEU CA C 54.92 0.1 1 207 73 73 LEU N N 123.78 0.1 1 208 74 74 ARG H H 8.49 0.1 1 209 74 74 ARG CA C 56.29 0.1 1 210 74 74 ARG N N 121.87 0.1 1 211 75 75 GLY H H 8.35 0.1 1 212 75 75 GLY CA C 45.01 0.1 1 213 75 75 GLY N N 109.78 0.1 1 214 76 76 GLY H H 8.08 0.1 1 215 76 76 GLY N N 108.66 0.1 1 stop_ save_